Thermally-induced atropisomerism promotes metal-organic cage construction

Molecular folding regulation with environmental stimuli is critical in living and artificial molecular machine systems. Herein, we described a macrocycle, cyclo[4] (1,3-(4,6-dimethyl)benzene)[4](1,3-(4,6-dimethyl)benzene)(4-pyridine). Under 298 K, it has three stable stiff atropisomers with names as 1 (Cs symmetry), 2 (Cs symmetry), and 3 (C4v symmetry). At 393 K, 1 can reversibly transform into 2, but at 473 K, it can irrevocably transform into 3. At 338 K, 3 and (PhCN)2PdCl2 complex to produce the metal-organic cage 4. Only at 338 K does the combination of 1 or 2 and (PhCN)2PdCl2 create a gel-like structure. Heating both gels to 473 K transforms them into 4. In addition to offering a thermally accelerated method for modifying self-assembled systems using macrocyclic building blocks, this study also has the potential to develop the nanoscale transformation material with a thermal response.

Other matters: 1) I think the title of the work is misleading.It is more like: Thermally-induced atropisomerism promotes/allows metal-organic cage construction.(Or something similar) 2) I found Figure 3 a little unclear.Too much blue is used obscuring the N atoms.The use of the blue plane to identify the symmetry plane is also not helpful.
3) The authors are keen to claim that several aspects of their work are 'first' examples.These claims should be modulated either to highlight some interesting point relative to other work or just be removed.It only distracts from their description of the present study.4) As mentioned above, some characterization of the gel states should be provided.Supplementary Information of this paper is comprehensive but would benefit from this data.5) ORTEP and diagrams showing any significant packing motifs of the atropoisomers in their crystal structures should be given in the supplementary information.6) English language should be revised throughout.
Reviewer #2: Remarks to the Author: The authors report a very interesting study into macrocycle synthesis, thermal interconversion and investigations into self-assembly under a range of conditions.The arguments presented are supported by a wide range of experimental approaches and the work is potentially suitable for publication in Nature Communications if the manuscript can be improved.
The paper would benefit from a very thorough proof read to pick up typographical issues, the use of incorrect words (e.g.porosity instead of pores) and other common issues.The text would benefit in certain sections from being less stop-start, greatly improving the reading experience.Other issues around units, cell parameters quoted not having esd values and almost illegible text on figures need to be addressed prior to publication.Finally, the references related to calixarenes would benefit form including the recent Atwood paper concerned with isolating spectacular nano capsules of unprecedented internal volume (https://pubs.rsc.org/en/content/articlelanding/2023/sc/d3sc01629c).
Reviewer #3: Remarks to the Author: Manuscript of Gong and co-workers describes the synthesis and characterization of three macrocyclic atropisomers, which can be interconverted into the most symmetric one by thermal treatment.In addition, these three macrocycles have been treated with Pd2+, leading to metal-organic complexes, two in oligomeric/polymeric structures, while the symmetric macrocycle leads to a nanocage.Notably, the authors suggest that the oligo/polymeric structures can be tune to the nanocage by thermal treatment.The manuscript contains many mistakes, and, at the moment, I do not find some potential application of this system.In addition, considering that recently a similar macrocyclic compound has been reported (Chem.Commun., 2019, 55, 3701-3704), I believe that this manuscript lacks of the novelty required by Nature Communication.Thus, I suggest the submission in a more specialized journal.
However, some issues need to be addressed: • abstract is not clear: in particular, it is not clear if the Pd metal ion is present in the original macrocycles or it has been added after.• Introduction, line 65: I suggest to read some recent reports JACS 2023, 145, 2822-2829; JACS  2021, 143, 35, 14136-14146; Acc.Chem.Res.2020, 53, 10, 2336-2346; Chem.Sci., 2020,11, 9617-9622;  • Introduction, line 81: the authors highlight the novelty of this system also because "this is the first example of thermally responsive nanoscale transformation from macrocycle to its self-assembly", however I suggest to read Chem.Commun., 2016, 52, 11681-11684;  • Supporting information, Figure S5: the intensity of 1H NMR spectrum is too low.Some impurities can be present in the sample.In addition, numeration of figures in the Supporting information is not progressive (Figure S32 is repeated 2 times); • quality of Scheme 2 must be improved.In addition, in the main text this is called Scheme, while in the caption is Figure .Reagent 4 is repeated 2 times; • caption of Figure 4 needs to be modified: C4v-CP4 is in the middle, Cs in the bottom and Cs' is up; • line 174: these references are not pertinent; • Line 182: why celite or NaCl substrates have been used? in addition, in Figure S46, the temperature indicated is 473K, while in the main text 573K (line 183).Furthermore, this Figure (S46) does not show the TOTAL CONVERTION into C4v.Please clarify, also indicating the difference between right and left TLC, the solid support used.
• why nitrobenze has been used?probably for the temperature range...? please, specify.
• spectra reported in Figure S52 seem to be acquired in different solvent: in particular, the right spectrum contain nitrobenzene, while the left one not.
• Line 328: NMR titration does not indicate the formation of polymeric structures, some additional experiments should be indicated (like GPC).I suggest to change "indicate" with "suggest".
• Line 343: in Figure S51, I do not believe that the three spectra are similar.I found many differences: aromatic region (ca.9 ppm); in the region between 6.5 and 7 ppm; • Probably, a part of Cs and Cs' tune to C4v, and this portion is visible to NMR and DOSY measurements can be performed.However, not all the isomers tune to the cage.Can the authors support the total conversion into the cage?• "Discussion" must be replaced with "Conclusions" Specific changes made in response to the commands of the reviewers are as below: Point-by-point response to referee 1: 1) The authors make persistent claims about several aspects of this work fulfilling some lack in the existing literature.However, this is not always true.In particular, they claim that there are no thermally activated atropisomers systems (Ln 178-179) although there are several reported in the tetraphenylporphyrin system and it has been studied extensively during the last few decades (for a very recent example see Martin et al Inorg. Chem. 2021, 60(7), 5240.
Response: Thanks very much for the kind remind.We scaned some literature and added to the revised manuscript as below: "However, the complex conformer distribution and conversion especially in solution studies between more than two rigid atropisomers are still lacking. 33" is revised to "However, the complex atropisomer distribution and conversion between more than two rigid atropisomers are still lacking.60, 5240-5251 (2021).
2) Although the present case isomers can be converted to the stable isomer, this system is reminiscent of the resorcinarene systems whose isomers are generally not interconvertible.Regardless, the analogy is notable in terms of the forms of the respective molecules, i.e., chair vs. kite vs crown isomers.Also, the NMR spectra shown in Fig 4 show trends in peak structure which are remarkably similar to mesosubstituted resorcinarenes.
Response: Appreciate so much for the kind suggestion.We compare the CP4 system with the resorcinarenes and then described their similarity in the revised manuscript as below: It is noted that the respective CP4 isomers are analogous to meso-substituted resorcinarenes with chair (Cs'-CP4), kite (Cs-CP4), or crown (C4v-CP4) structure. 35d additional reference as: 3) The 'interconversion' process is quite interesting, as described in the Figures 5 and 6 and associated text.However, there seems to be some statements missing.As I understand it, isomers Cs' and Cs are metastable states but do not convert to C4v in TCE at lower T.In nitrobenzene, however, the conversion to the most stable isomer is promoted and exclusive.Is there then any solvent dependence of the atropoisomer conversion or is it purely temperature-dependent?As mentioned in point (1), a comparison of this process with known atropoisomers and the rotisomerization processes would be beneficial.

Response:
We appreciate the reviewer for the commands.
We tested the time-dependent 1 H NMR spectra of CP4 in PhNO2-d5 at 393 K to determine whether there is a solvent effect in the conversion between the atropoisomers of CP4.It is found that there is solvent effect shown in the conversion between the atropoisomers, but the thermal dependence is still the major factor.We have described the detail in the revised manuscript and ESI as below: In manuscript: At 393 K, the spectra of Cs'-CP4 in PhNO2-d5 show gradually weakening signals and generate Cs-CP4 signals with increasing intensity ratio until the balance after 6 min (Figure 5b).Then the ratio between Cs-and Cs'-CP4 kept as 88:12.After heating Cs-CP4 solution for 1 min at 393 K, Cs'-CP4 signals appear and the system reaches dynamic equilibrium with a similar ratio between Cs-and Cs'-CP4 as 87: 13 (Figure S45, S47).It is noted that at 393 K, the reversible conversion between Cs-and Cs'-CP4 happened without C4v-CP4 participation (Figure 5a-5c, Figure S44, S46).The possible reason is the temperature is too low to induce Cs-or Cs'-CP4 passing across the energy barrier for C4v-CP4 formation.The transition between Cs-and Cs'-CP4 at 393 K was regarded as a first-order reversible reaction.According to the standard equilibrium (eq.1-1), the thermal dynamics and kinetic parameters of the transition were calculated using time-dependent 1 H NMR data.These parametes include the reaction rate constants (k1 = (1.4 ± 0.1) × 10 -2 s -1 , k-1 = -(2.3± 0.1) × 10 3 s -1 ), the Gibbs activated free energy (∆G 1 ≠ (393 K) as 111 ± 6 KJ/M ), the equilibrium constant (K1 as 6.1 ± 0.2 ), and the Gibbs free energy (∆G 1 θ (393 K) as -5.9 ± 0.2 KJ/M).With the formation energy of Cs'-CP4 as standard 0, the energy diagram of the transition between Cs-and Cs'-CP4 in PhNO2-d5 at 393 K can be obtained in Figure 5d Comparing the conversion parameters from Cs'-to Cs-CP4 in PhNO2-d5 or TCE-d2 at 393 K, it is found that the reaction rate of PhNO2-d5 (k1 as (1.4 ± 0.1) × 10 -2 s -1 ) is faster than that in TCE-d2 (k1 = ((5.2± 0.4) × 10 -3 s -1 ).There is only similar reversible conversion process between Cs-and Cs'-CP4 (without C4v-CP4 participation) in both cases.It is implied that, at the same temperature, the solvent can affect the same isomerization process, including kinetic and thermodynamic properties, but can not drive the reaction with a higher energy barrier (e.g., the conversion from Cs-or Cs'-to C4v-CP4).The conversion process in CP4 cage is compared with known atropoisomers and the rotisomerization processes in the revised manuscript as below: In manuscript: Compared with the reported cyclo [8](1,3-(4,6-dimethyl)benzene) (CDMB-8) involving two rigid atropisomers, 3 the introduction of pyridine groups in CP4 case increases the room temperature stable atropisomer kinds as three.Furthermore, as shown in the CP4 system, lower temperature (393 K) induced reversible transformation between metastable atroisomers, and higher temperature (473 K) induced irreversible transformation from metastable forms to stable conformation.This result is not present in the CDMB-8 system.Furthermore, temperature not less than 473 K was needed in typical rigid atropisomer conversion, including porphyrin, 62 [4]cyclo-chrysene, 12 or [n]cyclo-4,10-pyrenylenes 63 etc. conversion.In CP4 case, much lower temperature (393 K) is required for rapid conversion between the metastable atropisomer.
Furthermore, compard with CDMB-8, there is no change on the entire molecular skeleton and the neighboring methyl groups around the flip bond (σ bond) involved in the conformational transition.It is noteworthy that the insertion of the long-range groups (i.e., pyridinyl) on CP4 leads the difference between CP4 and CDMB-8, including the type of isomer, the transition temperature, also transition process.
Compared with other macrocyclic molecules (e.g., calixarene, porphyrin, or cyclic arene) which have been extensively studied at present, chemical modifications 15,63,64 are generally required to introduce different substituents for conformation fixing.In these systems, comformer regulation requires the participation of the guest, 10,11,15 pH regulation, 18 high temperature, 62 etc.The example of CP4, which can achieve transformation control between room temperature stable conformers only through heat, complements the regulation strategy of macrocyclic structures.
And additional reference as: 62. Ishizuka, T., Tanaka, S., Uchida, S., Wei, L. & Kojima, T. Selective Convergence to Atropisomers of a Porphyrin Derivative Having Bulky Substituents at the Periphery.J. Org.Chem.85, 12856-12869 (2020).4) Having established that the stable isomer is C4v, the authors then go on to synthesize an impressive cage structure based on the well-known Pd12 structural motif.What is the yield of this species?
Response: Thanks very much for the regarding.Yield and related PXRD characterization of larger-scale CC-Pd synthesis are given in the revised manuscript and ESI as below: In manuscript: Larger-scale synthesize of CC-Pd was carried out.C4v-CP4 (20 mg) created 24 mg CC-Pd sample with yield as 75% (see Figure S56).The PXRD analysis shows the pattern of larger-scale sample is similar as the simulated pattern from CC-Pd single crystal structure, which implies the sample structure is consistant with CC-Pd single crystal.

75.0%).
In ESI: 5) In Figure 8, the authors show the gelatinous states of the non-C4v isomers in the presence of Pd 2+ but there is no characterization of these states, either spectroscopic or microscopic.Is this some non-specifically-structured gel (as suggested by the polymer proposed by the authors) or is there any detectable ordering such as fibre or particle structure.Is the thermal behaviour of this gel intimately linked with the atropisomerisation or is the gel dissolved, isomerization occurs in solution then the capsule forms?This is important for the thermal responsivity claimed by the authors.
Response: Thank you very much for your kind reminding.We added scanning electron microscopy (SEM), dynamic light scattering (DLS) and gel permeation chromatography (GPC) test and described these gel characterization results in the revised manuscript and ESI as bellow: In manuscript: Scanning electron microscopy (SEM) displayed all gels were formed with nanospheres or plates via.The microstructure contains a large number of micron pores (Figure S59).The dynamic light scattering (DLS) test showed that the particle sizes of Cs-CP4@2Pd or Cs'-CP4@2Pd are basically the same and much larger than the particle sizes of C4v-CP4@2Pd (Figure S60).The gel permeation chromatography (GPC) results implied the average molecular weight of the polymer formed between Cs-, or Cs'-CP4 and Pd 2+ is about 20 times of corresponding macrocycle (Figure S61-S62).All these results suggested that Cs-or Cs'-CP4 respectively form polymeric structures with Pd 2+ (namely Cs-CP4@2Pd or Cs'-CP4@2Pd, respectively).
In ESI:     Response: Thank you very much for the reviewer's comment and support.We have improved the title of the revised manuscript as below: Thermally-induced atropisomerism promotes metal-organic cage construction 2) I found Figure 3 a little unclear.Too much blue is used obscuring the N atoms.The use of the blue plane to identify the symmetry plane is also not helpful.
Response: Thank you very much for your comment and support.We have adjusted the colors in Figure 3 in the revised manuscript.As below: Response: Appreciate so much for your comment and support.We have changed "first" to "few", " unusual", or "complementary" in the revised manuscript as below: "At present, there are also first examples of reversible/irreversible transformation between three rigid atropisomers via simple thermal regulation." is revised as "At present, there are also few examples of reversible/irreversible transformation between three rigid atropisomers via simple thermal regulation.""To the best of our knowledge, this is an first example of thermally responsive nanoscale transformation from macrocycle to self-assembly." is revised as "To the best of our knowledge, this is an unusual example of thermally responsive nanoscale transformation from macrocycle to self-assembly."; "This work provides a novel strategy to control the structure and properties of macrocycles, as well as related self-assembled systems." is revised as "This work provides a complementary strategy to control the structure and properties of macrocycles, as well as related self-assembled systems."4) As mentioned above, some characterization of the gel states should be provided.Supplementary Information of this paper is comprehensive but would benefit from this data.
Response: Thanks very much for the comment and support.We added SEM (Figure R5), DLS (Figure R6) and GPC (Figure R7, R8) test in the revised manuscript and ESI as shown above in the response for point 5. 5) ORTEP and diagrams showing any significant packing motifs of the atropoisomers in their crystal structures should be given in the supplementary information.
Response: Thank you so much for your comments.We have improved the revised ESI with corresponding thermal ellipsoids and packing diagrams of each atropoisomer in their single crystal structure as below:   6) English language should be revised throughout.
Response: appreciate so much for your suggestions.We try our best to polish the manuscript carefully.

Point-by-point response to referee 2:
1) The paper would benefit from a very thorough proof read to pick up typographical issues, the use of incorrect words (e.g.porosity instead of pores) and other common issues.The text would benefit in certain sections from being less stop-start, greatly improving the reading experience.Other issues around units, cell parameters quoted not having esd values and almost illegible text on figures need to be addressed prior to publication.Finally, the references related to calixarenes would benefit form including the recent Atwood paper concerned with isolating spectacular nano capsules of unprecedented internal volume (https://pubs.rsc.org/en/content/articlelanding/2023/sc/d3sc01629c).
Response: Thank you very much for your comments and support.We have proofread the manuscript according to the requirements of Nature Communication and corrected the wrong content.We read Atwood's paper carefully, benefited a lot, and cited the paper as below: " The typical examples involved calixarenes, 28,42-48 pillar[n]arene, 49 and porphyrin,  Commun.52, 11681-11684 (2016).

Point-by-point response to referee 3:
Manuscript of Gong and co-workers describes the synthesis and characterization of three macrocyclic atropisomers, which can be interconverted into the most symmetric one by thermal treatment.In addition, these three macrocycles have been treated with Pd 2+ , leading to metal-organic complexes, two in oligomeric/polymeric structures, while the symmetric macrocycle leads to a nanocage.Notably, the authors suggest that the oligo/polymeric structures can be tune to the nanocage by thermal treatment.
The manuscript contains many mistakes, and, at the moment, I do not find some potential application of this system.In addition, considering that recently a similar macrocyclic compound has been reported (Chem.Commun., 2019, 55, 3701-3704), I believe that this manuscript lacks of the novelty required by Nature Communication.
Thus, I suggest the submission in a more specialized journal.
Response: Thank you very much for your comments, it is a great help to improve our article.
We suggested that the temperature-induced rigid conformational transformation of CP4 has potential applications in temperature responsive materials.The assembly and conversion formed between CP4 and Pd 2+ could be considered as inial example.
The CP4 case is quite different from the reported macrocyclic compound.We described it in the revised manuscript as below: Compared with the reported cyclo [8](1,3-(4,6-dimethyl)benzene) (CDMB-8) with two rigid atropisomers, 3 the introduction of pyridine groups in CP4 case increases the room temperature stable atropisomer kinds as three.Furthermore, as shown in the CP4 system, lower temperature (393 K) induced reversible transformation between metastable atroisomers, and higher temperature (473 K) induced irreversible transformation from metastable forms to stable conformation.This result is not present in the CDMB-8 system.Furthermore, temperature not less than 473 K was needed in typical rigid atropisomer conversion, including porphyrin, 62 [4]cyclo-chrysene, 12 or [n]cyclo-4,10-pyrenylenes 63 etc.In CP4 case, much lower temperature (393 K) is required for rapid conversion between the metastable atropisomer.Furthermore, compard with CDMB-8, there is no change on the entire molecular skeleton and the neighboring methyl groups around the flip bond (σ bond) involved in the conformational transition.It is noteworthy that the insertion of the long-range groups (i.e., pyridinyl) on CP4 leads the difference between CP4 and CDMB-8, including the type of isomer, the transition temperature, also transition process.
However, some issues need to be addressed: • abstract is not clear: in particular, it is not clear if the Pd metal ion is present in the original macrocycles or it has been added after.
Response: Thank you very much for your comments, Specific experimental procedures are supplemented in the revised manuscript as below: Abstract 28,61 " And additional reference as: 61 Martin, D. J., Mercado, B. Q. & Mayer, J. M. All Four Atropisomers of Iron Tetra(o-N,N,N-trimethylanilinium)porphyrin in Both the Ferric and Ferrous States.Inorg.Chem.

Figure R4 (
Figure R4 (Figure S56. in ESI).PXRD patterns of CC-Pd (black line) and simulation curve obtained from single crystal data (red line), respectively.
think the title of the work is misleading.It is more like: Thermally-induced atropisomerism promotes/allows metal-organic cage construction.(Or something similar)